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Add procedures mappings for MIMIC-IV v2.0 - SSSOM format #1419

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merged 3 commits into from
Apr 3, 2024

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a-chahin
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@a-chahin a-chahin commented Nov 8, 2022

This pull request adds two mapping csv files for procedures concepts from the d_items and procedureevents tables in MIMIC-IV v2.0. The first file procedureevents_to_snomed.csv contains itemid to SNOMED-CT mappings. The second file procedureevents_to_omop.csv contains itemid to OMOP mappings.

Both files use the simple standard for sharing ontology mappings SSSOM format @sssom

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Looks good, thanks @a-chahin!

  • I notice that you have left some of the author_id fields empty for the mappings. I assume this is because we inherited those mappings?
  • The documentation at https://mapping-commons.github.io/sssom/author_id/ suggests that author_id is "Recommended to be a (pipe-separated) list of ORCIDs". I think you are currently using commas to separate lists. Should we swap out the commas for |?
  • Minor thing, but both files are missing a newline character at the end. This can lead to some tools to ignore the final line. If you are editing the files, we might want to add a newline (just hit return at the end of the final line of each file).

@matentzn hope you don't mind me tagging you here! This file is a mapping for MIMIC-IV concepts. No pressure, but we would appreciate your thoughts on whether anything more should be done to conform to @sssom format.

@a-chahin
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a-chahin commented Nov 8, 2022

Looks good, thanks @a-chahin!

  • I notice that you have left some of the author_id fields empty for the mappings. I assume this is because we inherited those mappings?
  • The documentation at https://mapping-commons.github.io/sssom/author_id/ suggests that author_id is "Recommended to be a (pipe-separated) list of ORCIDs". I think you are currently using commas to separate lists. Should we swap out the commas for |?
  • Minor thing, but both files are missing a newline character at the end. This can lead to some tools to ignore the final line. If you are editing the files, we might want to add a newline (just hit return at the end of the final line of each file).

@matentzn hope you don't mind me tagging you here! This file is a mapping for MIMIC-IV concepts. No pressure, but we would appreciate your thoughts on whether anything more should be done to conform to @sssom format.

Thank you @tompollard!

  • You are correct. The author_id field is empty for concepts that were mapped by the OMOP folks.
  • Thank you for bringing this to my attention. I'm sorry I missed it.
  • I will fix the ORCIDs and add a newline character at the end and update the csv files.

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I have (1) added the missing newline and (2) changed the orcid list separator from , to |.

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Thanks @a-chahin !

@tompollard tompollard merged commit e58ecab into main Apr 3, 2024
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@tompollard tompollard deleted the procedures_v2.0 branch April 3, 2024 15:54
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